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Silverman A, Melamed S. Biological Insights from RNA-RNA Interactomes in Bacteria, as Revealed by RIL-seq. Methods Mol Biol 2025; 2866:189-206. [PMID: 39546204 DOI: 10.1007/978-1-0716-4192-7_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2024]
Abstract
Bacteria reside in constantly changing environments and require rapid and precise adjustments of gene expression to ensure survival. Small regulatory RNAs (sRNAs) are a crucial element that bacteria utilize to achieve this. sRNAs are short RNA molecules that modulate gene expression usually through base-pairing interactions with target RNAs, primarily mRNAs. These interactions can lead to either negative outcomes such as mRNA degradation or translational repression or positive outcomes such as mRNA stabilization or translation enhancement. In recent years, high-throughput approaches such as RIL-seq (RNA interaction by ligation and sequencing) revolutionized the sRNA field by enabling the identification of sRNA targets on a global scale, unveiling intricate sRNA-RNA networks. In this review, we discuss the insights gained from investigating sRNA-RNA networks in well-studied bacterial species as well as in understudied bacterial species. Having a complete understanding of sRNA-mediated regulation is critical for the development of new strategies for controlling bacterial growth and combating bacterial infections.
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Affiliation(s)
- Aviezer Silverman
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Sahar Melamed
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.
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2
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Kreis V, Toffano-Nioche C, Denève-Larrazet C, Marvaud JC, Garneau JR, Dumont F, van Dijk EL, Jaszczyszyn Y, Boutserin A, D'Angelo F, Gautheret D, Kansau I, Janoir C, Soutourina O. Dual RNA-seq study of the dynamics of coding and non-coding RNA expression during Clostridioides difficile infection in a mouse model. mSystems 2024; 9:e0086324. [PMID: 39601557 DOI: 10.1128/msystems.00863-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Accepted: 10/31/2024] [Indexed: 11/29/2024] Open
Abstract
Clostridioides difficile is the leading cause of healthcare-associated diarrhea in industrialized countries. Many questions remain to be answered about the mechanisms governing its interaction with the host during infection. Non-coding RNAs (ncRNAs) contribute to shape virulence in many pathogens and modulate host responses; however, their role in C. difficile infection (CDI) has not been explored. To better understand the dynamics of ncRNA expression contributing to C. difficile infectious cycle and host response, we used a dual RNA-seq approach in a conventional murine model. From the pathogen side, this transcriptomic analysis revealed the upregulation of virulence factors, metabolism, and sporulation genes, as well as the identification of 61 ncRNAs differentially expressed during infection that correlated with the analysis of available raw RNA-seq data sets from two independent studies. From these data, we identified 118 potential new transcripts in C. difficile, including 106 new ncRNA genes. From the host side, we observed the induction of several pro-inflammatory pathways, and among the 185 differentially expressed ncRNAs, the overexpression of microRNAs (miRNAs) previously associated to inflammatory responses or unknown long ncRNAs and miRNAs. A particular host gene expression profile could be associated to the symptomatic infection. In accordance, the metatranscriptomic analysis revealed specific microbiota changes accompanying CDI and specific species associated with symptomatic infection in mice. This first adaptation of in vivo dual RNA-seq to C. difficile contributes to unravelling the regulatory networks involved in C. difficile infectious cycle and host response and provides valuable resources for further studies of RNA-based mechanisms during CDI.IMPORTANCEClostridioides difficile is a major cause of nosocomial infections associated with antibiotic therapy classified as an urgent antibiotic resistance threat. This pathogen interacts with host and gut microbial communities during infection, but the mechanisms of these interactions remain largely to be uncovered. Noncoding RNAs contribute to bacterial virulence and host responses, but their expression has not been explored during C. difficile infection. We took advantage of the conventional mouse model of C. difficile infection to look simultaneously to the dynamics of gene expression in pathogen, its host, and gut microbiota composition, providing valuable resources for future studies. We identified a number of ncRNAs that could mediate the adaptation of C. difficile inside the host and the crosstalk with the host immune response. Promising inflammation markers and potential therapeutic targets emerged from this work open new directions for RNA-based and microbiota-modulatory strategies to improve the efficiency of C. difficile infection treatments.
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Affiliation(s)
- Victor Kreis
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Claire Toffano-Nioche
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | | | | | | | | | - Erwin L van Dijk
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Yan Jaszczyszyn
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Anaïs Boutserin
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Francesca D'Angelo
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Daniel Gautheret
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Imad Kansau
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Orsay, France
| | - Claire Janoir
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Orsay, France
| | - Olga Soutourina
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
- Institut Universitaire de France (IUF), Paris, France
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3
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Lenče T, Sulzer J, Andress K, Gribling-Burrer AS, Lamm-Schmidt V, Barquist L, Smyth RP, Faber F. The conserved noncoding RNA ModT coordinates growth and virulence in Clostridioides difficile. PLoS Biol 2024; 22:e3002948. [PMID: 39671441 DOI: 10.1371/journal.pbio.3002948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2024] [Accepted: 11/22/2024] [Indexed: 12/15/2024] Open
Abstract
Bacterial noncoding RNAs fulfill a variety of cellular functions as catalysts, as scaffolds in protein complexes or as regulators of gene expression. They often exhibit complex tertiary structures that are a key determinant of their biochemical function. Here, we characterize the structured "raiA motif" RNA from Clostridioides difficile, which is conserved in more than 2,500 bacterial species from the phyla Bacillota and Actinomycetota. We show that its transcript abundance and stability in exponentially growing bacteria rivals that of ribosomal RNAs. Deletion of the "raiA motif" RNA is associated with delayed transition into stationary phase, and changes in stationary phase pathways such as spore formation, hence we rename it ModT (modulator of transition phase). Mechanistically, we show that ModT-mediated changes in cellular cyclic di-GMP levels are linked to the pronounced sporulation defect in the modT mutant. Importantly, we show that expression profiles and isoform patterns of ModT are conserved in Clostridium perfringens and Paeniclostridium sordellii, and that these orthologs can functionally complement ModT in C. difficile. Chemical structure probing of ModT in vivo reveals dynamic refolding and provides initial evidence for a potential association of ModT with proteins. In summary, our findings indicate that ModT fulfills a conserved role in regulating growth transitions in bacteria and provide a crucial step towards delineating its molecular mechanism.
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Affiliation(s)
- Tina Lenče
- University of Würzburg, Faculty of Medicine, Institute of Molecular Infection Biology, Würzburg, Germany
| | - Johannes Sulzer
- University of Würzburg, Faculty of Medicine, Institute of Molecular Infection Biology, Würzburg, Germany
| | - Kilian Andress
- University of Würzburg, Faculty of Medicine, Institute of Molecular Infection Biology, Würzburg, Germany
| | - Anne-Sophie Gribling-Burrer
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Vanessa Lamm-Schmidt
- University of Würzburg, Faculty of Medicine, Institute of Molecular Infection Biology, Würzburg, Germany
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
- University of Würzburg, Faculty of Medicine, Würzburg, Germany
- Department of Biology, University of Toronto, Mississauga, Ontario, Canada
| | - Redmond P Smyth
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
- University of Würzburg, Faculty of Medicine, Würzburg, Germany
| | - Franziska Faber
- University of Würzburg, Faculty of Medicine, Institute of Molecular Infection Biology, Würzburg, Germany
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
- University of Würzburg, Faculty of Medicine, Institute for Hygiene and Microbiology, Würzburg, Germany
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4
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Hasan MK, Alaribe O, Govind R. Regulatory networks: Linking toxin production and sporulation in Clostridioides difficile. Anaerobe 2024; 91:102920. [PMID: 39521117 DOI: 10.1016/j.anaerobe.2024.102920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2024] [Revised: 10/29/2024] [Accepted: 10/31/2024] [Indexed: 11/16/2024]
Abstract
Clostridioides difficile has been recognized as an important nosocomial pathogen that causes diarrheal disease as a consequence of antibiotic exposure and costs the healthcare system billions of dollars every year. C. difficile enters the host gut as dormant spores, germinates into vegetative cells, colonizes the gut, and produces toxins TcdA and/or TcdB, leading to diarrhea and inflammation. Spores are the primary transmission vehicle, while the toxins A and B directly contribute to the disease. Thus, toxin production and sporulation are the key traits that determine the success of C. difficile as a pathogen. Both toxins and spores are produced during the late stationary phase in response to various stimuli. This review provides a comprehensive analysis of the current knowledge on the molecular mechanisms, highlighting the regulatory pathways that interconnect toxin gene expression and sporulation in C. difficile. The roles of carbohydrates, amino acids and other nutrients and signals, in modulating these virulence traits through global regulatory networks are discussed. Understanding the links within the gene regulatory network is crucial for developing effective therapeutic strategies against C. difficile infections, potentially leading to targeted interventions that disrupt the co-regulation of toxin production and sporulation.
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Affiliation(s)
- Md Kamrul Hasan
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
| | - Oluchi Alaribe
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
| | - Revathi Govind
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA.
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5
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Badilla Lobo A, Soutourina O, Peltier J. The current riboswitch landscape in Clostridioides difficile. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001508. [PMID: 39405103 PMCID: PMC11477304 DOI: 10.1099/mic.0.001508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2024] [Accepted: 09/26/2024] [Indexed: 10/19/2024]
Abstract
Riboswitches are 5' RNA regulatory elements that are capable of binding to various ligands, such as small metabolites, ions and tRNAs, leading to conformational changes and affecting gene transcription or translation. They are widespread in bacteria and frequently control genes that are essential for the survival or virulence of major pathogens. As a result, they represent promising targets for the development of new antimicrobial treatments. Clostridioides difficile, a leading cause of antibiotic-associated nosocomial diarrhoea in adults, possesses numerous riboswitches in its genome. Accumulating knowledge of riboswitch-based regulatory mechanisms provides insights into the potential therapeutic targets for treating C. difficile infections. This review offers an in-depth examination of the current state of knowledge regarding riboswitch-mediated regulation in C. difficile, highlighting their importance in bacterial adaptability and pathogenicity. Particular attention is given to the ligand specificity and function of known riboswitches in this bacterium. The review also discusses the recent progress that has been made in the development of riboswitch-targeting compounds as potential treatments for C. difficile infections. Future research directions are proposed, emphasizing the need for detailed structural and functional analyses of riboswitches to fully harness their regulatory capabilities for developing new antimicrobial strategies.
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Affiliation(s)
- Adriana Badilla Lobo
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Olga Soutourina
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Johann Peltier
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
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6
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Wu K, Lin X, Lu Y, Dong R, Jiang H, Svensson SL, Zheng J, Shen N, Camilli A, Chao Y. RNA interactome of hypervirulent Klebsiella pneumoniae reveals a small RNA inhibitor of capsular mucoviscosity and virulence. Nat Commun 2024; 15:6946. [PMID: 39138169 PMCID: PMC11322559 DOI: 10.1038/s41467-024-51213-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 08/01/2024] [Indexed: 08/15/2024] Open
Abstract
Hypervirulent Klebsiella pneumoniae (HvKP) is an emerging bacterial pathogen causing invasive infection in immune-competent humans. The hypervirulence is strongly linked to the overproduction of hypermucoviscous capsule, but the underlying regulatory mechanisms of hypermucoviscosity (HMV) have been elusive, especially at the post-transcriptional level mediated by small noncoding RNAs (sRNAs). Using a recently developed RNA interactome profiling approach iRIL-seq, we interrogate the Hfq-associated sRNA regulatory network and establish an intracellular RNA-RNA interactome in HvKP. Our data reveal numerous interactions between sRNAs and HMV-related mRNAs, and identify a plethora of sRNAs that repress or promote HMV. One of the strongest HMV repressors is ArcZ, which is activated by the catabolite regulator CRP and targets many HMV-related genes including mlaA and fbp. We discover that MlaA and its function in phospholipid transport is crucial for capsule retention and HMV, inactivation of which abolishes Klebsiella virulence in mice. ArcZ overexpression drastically reduces bacterial burden in mice and reduces HMV in multiple hypervirulent and carbapenem-resistant clinical isolates, indicating ArcZ is a potent RNA inhibitor of bacterial pneumonia with therapeutic potential. Our work unravels a novel CRP-ArcZ-MlaA regulatory circuit of HMV and provides mechanistic insights into the posttranscriptional virulence control in a superbug of global concern.
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Affiliation(s)
- Kejing Wu
- Microbial RNA Systems Biology Unit, Center for Microbes, Development and Health (CMDH), Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Xingyu Lin
- Microbial RNA Systems Biology Unit, Center for Microbes, Development and Health (CMDH), Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yujie Lu
- Microbial RNA Systems Biology Unit, Center for Microbes, Development and Health (CMDH), Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Rui Dong
- Microbial RNA Systems Biology Unit, Center for Microbes, Development and Health (CMDH), Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Hongnian Jiang
- Microbial RNA Systems Biology Unit, Center for Microbes, Development and Health (CMDH), Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Sarah L Svensson
- Microbial RNA Systems Biology Unit, Center for Microbes, Development and Health (CMDH), Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Jiajia Zheng
- Center of Infectious Disease, Peking University Third Hospital, Beijing, China
| | - Ning Shen
- Center of Infectious Disease, Peking University Third Hospital, Beijing, China
| | - Andrew Camilli
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA
| | - Yanjie Chao
- Microbial RNA Systems Biology Unit, Center for Microbes, Development and Health (CMDH), Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Key Laboratory of RNA Innovation, Science and Engineering (RISE), Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China.
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7
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Youngblom MA, Smith TM, Murray HJ, Pepperell CS. Adaptation of the Mycobacterium tuberculosis transcriptome to biofilm growth. PLoS Pathog 2024; 20:e1012124. [PMID: 38635841 PMCID: PMC11060545 DOI: 10.1371/journal.ppat.1012124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 04/30/2024] [Accepted: 03/14/2024] [Indexed: 04/20/2024] Open
Abstract
Mycobacterium tuberculosis (M. tb), the causative agent of tuberculosis (TB), is a leading global cause of death from infectious disease. Biofilms are increasingly recognized as a relevant growth form during M. tb infection and may impede treatment by enabling bacterial drug and immune tolerance. M. tb has a complicated regulatory network that has been well-characterized for many relevant disease states, including dormancy and hypoxia. However, despite its importance, our knowledge of the genes and pathways involved in biofilm formation is limited. Here we characterize the biofilm transcriptomes of fully virulent clinical isolates and find that the regulatory systems underlying biofilm growth vary widely between strains and are also distinct from regulatory programs associated with other environmental cues. We used experimental evolution to investigate changes to the transcriptome during adaptation to biofilm growth and found that the application of a uniform selection pressure resulted in loss of strain-to-strain variation in gene expression, resulting in a more uniform biofilm transcriptome. The adaptive trajectories of transcriptomes were shaped by the genetic background of the M. tb population leading to convergence on a sub-lineage specific transcriptome. We identified widespread upregulation of non-coding RNA (ncRNA) as a common feature of the biofilm transcriptome and hypothesize that ncRNA function in genome-wide modulation of gene expression, thereby facilitating rapid regulatory responses to new environments. These results reveal a new facet of the M. tb regulatory system and provide valuable insight into how M. tb adapts to new environments.
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Affiliation(s)
- Madison A. Youngblom
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Madison-Wisconsin, Madison, Wisconsin, United States of America
| | - Tracy M. Smith
- Department of Medicine (Infectious Diseases), School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Holly J. Murray
- Department of Medicine (Infectious Diseases), School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Caitlin S. Pepperell
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Madison-Wisconsin, Madison, Wisconsin, United States of America
- Department of Medicine (Infectious Diseases), School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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8
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McQuail J, Matera G, Gräfenhan T, Bischler T, Haberkant P, Stein F, Vogel J, Wigneshweraraj S. Global Hfq-mediated RNA interactome of nitrogen starved Escherichia coli uncovers a conserved post-transcriptional regulatory axis required for optimal growth recovery. Nucleic Acids Res 2024; 52:2323-2339. [PMID: 38142457 PMCID: PMC10954441 DOI: 10.1093/nar/gkad1211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 11/17/2023] [Accepted: 12/20/2023] [Indexed: 12/26/2023] Open
Abstract
The RNA binding protein Hfq has a central role in the post-transcription control of gene expression in many bacteria. Numerous studies have mapped the transcriptome-wide Hfq-mediated RNA-RNA interactions in growing bacteria or bacteria that have entered short-term growth-arrest. To what extent post-transcriptional regulation underpins gene expression in growth-arrested bacteria remains unknown. Here, we used nitrogen (N) starvation as a model to study the Hfq-mediated RNA interactome as Escherichia coli enter, experience, and exit long-term growth arrest. We observe that the Hfq-mediated RNA interactome undergoes extensive changes during N starvation, with the conserved SdsR sRNA making the most interactions with different mRNA targets exclusively in long-term N-starved E. coli. Taking a proteomics approach, we reveal that in growth-arrested cells SdsR influences gene expression far beyond its direct mRNA targets. We demonstrate that the absence of SdsR significantly compromises the ability of the mutant bacteria to recover growth competitively from the long-term N-starved state and uncover a conserved post-transcriptional regulatory axis which underpins this process.
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Affiliation(s)
- Josh McQuail
- Section of Molecular Microbiology and Centre for Bacterial Resistance Biology, Faculty of Medicine, Imperial College London, UK
| | - Gianluca Matera
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080 Würzburg, Germany
| | - Tom Gräfenhan
- Core Unit Systems Medicine, University of Würzburg, D-97080 Würzburg, Germany
| | - Thorsten Bischler
- Core Unit Systems Medicine, University of Würzburg, D-97080 Würzburg, Germany
| | - Per Haberkant
- Proteomics Core Facility, EMBL Heidelberg, D-69117,Heidelberg, Germany
| | - Frank Stein
- Proteomics Core Facility, EMBL Heidelberg, D-69117,Heidelberg, Germany
| | - Jörg Vogel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080 Würzburg, Germany
- Institute for Molecular Infection Biology (IMIB), Faculty of Medicine, University of Würzburg, D-97080 Würzburg, Germany
| | - Sivaramesh Wigneshweraraj
- Section of Molecular Microbiology and Centre for Bacterial Resistance Biology, Faculty of Medicine, Imperial College London, UK
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9
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Pensinger DA, Dobrila HA, Stevenson DM, Hryckowian ND, Amador-Noguez D, Hryckowian AJ. Exogenous butyrate inhibits butyrogenic metabolism and alters virulence phenotypes in Clostridioides difficile. mBio 2024; 15:e0253523. [PMID: 38289141 PMCID: PMC10936429 DOI: 10.1128/mbio.02535-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 12/20/2023] [Indexed: 02/13/2024] Open
Abstract
The gut microbiome engenders colonization resistance against the diarrheal pathogen Clostridioides difficile, but the molecular basis of this colonization resistance is incompletely understood. A prominent class of gut microbiome-produced metabolites important for colonization resistance against C. difficile is short-chain fatty acids (SCFAs). In particular, one SCFA (butyrate) decreases the fitness of C. difficile in vitro and is correlated with C. difficile-inhospitable gut environments, both in mice and in humans. Here, we demonstrate that butyrate-dependent growth inhibition in C. difficile occurs under conditions where C. difficile also produces butyrate as a metabolic end product. Furthermore, we show that exogenous butyrate is internalized into C. difficile cells and is incorporated into intracellular CoA pools where it is metabolized in a reverse (energetically unfavorable) direction to crotonyl-CoA and (S)-3-hydroxybutyryl-CoA and/or 4-hydroxybutyryl-CoA. This internalization of butyrate and reverse metabolic flow of a butyrogenic pathway(s) in C. difficile coincides with alterations in toxin release and sporulation. Together, this work highlights butyrate as a marker of a C. difficile-inhospitable environment to which C. difficile responds by releasing its diarrheagenic toxins and producing environmentally resistant spores necessary for transmission between hosts. These findings provide foundational data for understanding the molecular and genetic basis of how C. difficile growth is inhibited by butyrate and how butyrate alters C. difficile virulence in the face of a highly competitive and dynamic gut environment.IMPORTANCEThe gut microbiome engenders colonization resistance against the diarrheal pathogen Clostridioides difficile, but the molecular basis of this colonization resistance is incompletely understood, which hinders the development of novel therapeutic interventions for C. difficile infection (CDI). We investigated how C. difficile responds to butyrate, an end-product of gut microbiome community metabolism which inhibits C. difficile growth. We show that exogenously produced butyrate is internalized into C. difficile, which inhibits C. difficile growth by interfering with its own butyrate production. This growth inhibition coincides with increased toxin release from C. difficile cells and the production of environmentally resistant spores necessary for transmission between hosts. Future work to disentangle the molecular mechanisms underlying these growth and virulence phenotypes will likely lead to new strategies to restrict C. difficile growth in the gut and minimize its pathogenesis during CDI.
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Affiliation(s)
- Daniel A. Pensinger
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
- Department of Medical Microbiology & Immunology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Horia A. Dobrila
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
- Department of Medical Microbiology & Immunology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - David M. Stevenson
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Nicole D. Hryckowian
- Department of Medical Microbiology & Immunology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Daniel Amador-Noguez
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Andrew J. Hryckowian
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
- Department of Medical Microbiology & Immunology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
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10
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Ruhland E, Siemers M, Gerst R, Späth F, Vogt LN, Figge MT, Papenfort K, Fröhlich KS. The global RNA-RNA interactome of Klebsiella pneumoniae unveils a small RNA regulator of cell division. Proc Natl Acad Sci U S A 2024; 121:e2317322121. [PMID: 38377209 PMCID: PMC10907235 DOI: 10.1073/pnas.2317322121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 01/18/2024] [Indexed: 02/22/2024] Open
Abstract
The ubiquitous RNA chaperone Hfq is involved in the regulation of key biological processes in many species across the bacterial kingdom. In the opportunistic human pathogen Klebsiella pneumoniae, deletion of the hfq gene affects the global transcriptome, virulence, and stress resistance; however, the ligands of the major RNA-binding protein in this species have remained elusive. In this study, we have combined transcriptomic, co-immunoprecipitation, and global RNA interactome analyses to compile an inventory of conserved and species-specific RNAs bound by Hfq and to monitor Hfq-mediated RNA-RNA interactions. In addition to dozens of RNA-RNA pairs, our study revealed an Hfq-dependent small regulatory RNA (sRNA), DinR, which is processed from the 3' terminal portion of dinI mRNA. Transcription of dinI is controlled by the master regulator of the SOS response, LexA. As DinR accumulates in K. pneumoniae in response to DNA damage, the sRNA represses translation of the ftsZ transcript by occupation of the ribosome binding site. Ectopic overexpression of DinR causes depletion of ftsZ mRNA and inhibition of cell division, while deletion of dinR antagonizes cell elongation in the presence of DNA damage. Collectively, our work highlights the important role of RNA-based gene regulation in K. pneumoniae and uncovers the central role of DinR in LexA-controlled division inhibition during the SOS response.
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Affiliation(s)
- Eric Ruhland
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena07743, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena07743, Germany
| | - Malte Siemers
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena07743, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena07743, Germany
| | - Ruman Gerst
- Faculty of Biological Sciences, Friedrich Schiller University, Jena07743, Germany
- Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology–Hans Knöll Institute, Jena07745, Germany
| | - Felix Späth
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena07743, Germany
| | - Laura Nicole Vogt
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena07743, Germany
| | - Marc Thilo Figge
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena07743, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena07743, Germany
- Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology–Hans Knöll Institute, Jena07745, Germany
| | - Kai Papenfort
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena07743, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena07743, Germany
| | - Kathrin Sophie Fröhlich
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena07743, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena07743, Germany
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11
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Edwards AN, McBride SM. The RgaS-RgaR two-component system promotes Clostridioides difficile sporulation through a small RNA and the Agr1 system. PLoS Genet 2023; 19:e1010841. [PMID: 37844084 PMCID: PMC10602386 DOI: 10.1371/journal.pgen.1010841] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 10/26/2023] [Accepted: 10/02/2023] [Indexed: 10/18/2023] Open
Abstract
The ability to form a dormant spore is essential for the survival of the anaerobic pathogen, Clostridioides difficile, outside of the mammalian gastrointestinal tract. The initiation of sporulation is governed by the master regulator of sporulation, Spo0A, which is activated by phosphorylation. Multiple sporulation factors control Spo0A phosphorylation; however, this regulatory pathway is not well defined in C. difficile. We discovered that RgaS and RgaR, a conserved orphan histidine kinase and orphan response regulator, function together as a cognate two-component regulatory system to directly activate transcription of several genes. One of these targets, agrB1D1, encodes gene products that synthesize and export a small quorum-sensing peptide, AgrD1, which positively influences expression of early sporulation genes. Another target, a small regulatory RNA now known as SpoZ, impacts later stages of sporulation through a small hypothetical protein and an additional, unknown regulatory mechanism(s). Unlike Agr systems in many organisms, AgrD1 does not activate the RgaS-RgaR two-component system, and thus, is not responsible for autoregulating its own production. Altogether, we demonstrate that C. difficile utilizes a conserved two-component system that is uncoupled from quorum-sensing to promote sporulation through two distinct regulatory pathways.
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Affiliation(s)
- Adrianne N. Edwards
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, Georgia, United States of America
| | - Shonna M. McBride
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, Georgia, United States of America
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Pensinger DA, Dobrila HA, Stevenson DM, Davis NM, Amador-Noguez D, Hryckowian AJ. Exogenous butyrate inhibits butyrogenic metabolism and alters expression of virulence genes in Clostridioides difficile. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.06.548018. [PMID: 37461482 PMCID: PMC10350080 DOI: 10.1101/2023.07.06.548018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
The gut microbiome engenders colonization resistance against the diarrheal pathogen Clostridioides difficile but the molecular basis of this colonization resistance is incompletely understood. A prominent class of gut microbiome-produced metabolites important for colonization resistance against C. difficile is short chain fatty acids (SCFAs). In particular, one SCFA (butyrate) decreases the fitness of C. difficile in vitro and is correlated with C. difficile-inhospitable gut environments, both in mice and in humans. Here, we demonstrate that butyrate-dependent growth inhibition in C. difficile occurs under conditions where C. difficile also produces butyrate as a metabolic end product. Furthermore, we show that exogenous butyrate is internalized into C. difficile cells, is incorporated into intracellular CoA pools where it is metabolized in a reverse (energetically unfavorable) direction to crotonyl-CoA and (S)-3-hydroxybutyryl-CoA and/or 4-hydroxybutyryl-CoA. This internalization of butyrate and reverse metabolic flow of butyrogenic pathway(s) in C. difficile coincides with alterations in toxin production and sporulation. Together, this work highlights butyrate as a signal of a C. difficile inhospitable environment to which C. difficile responds by producing its diarrheagenic toxins and producing environmentally-resistant spores necessary for transmission between hosts. These findings provide foundational data for understanding the molecular and genetic basis of how C. difficile growth is inhibited by butyrate and how butyrate serves as a signal to alter C. difficile virulence in the face of a highly competitive and dynamic gut environment.
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Affiliation(s)
- Daniel A. Pensinger
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Department of Medical Microbiology & Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Horia A. Dobrila
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Department of Medical Microbiology & Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - David M. Stevenson
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Nicole M. Davis
- Department of Medical Microbiology & Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | | | - Andrew J. Hryckowian
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Department of Medical Microbiology & Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
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13
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Edwards AN, McBride SM. The RgaS-RgaR two-component system promotes Clostridioides difficile sporulation through a small RNA and the Agr1 system. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.26.546640. [PMID: 37425791 PMCID: PMC10327067 DOI: 10.1101/2023.06.26.546640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
The ability to form a dormant spore is essential for the survival of the anaerobic, gastrointestinal pathogen Clostridioides difficile outside of the mammalian gastrointestinal tract. The initiation of sporulation is governed by the master regulator of sporulation, Spo0A, which is activated by phosphorylation. Multiple sporulation factors control Spo0A phosphorylation; however, this regulatory pathway is not well defined in C. difficile. We discovered that RgaS and RgaR, a conserved orphan histidine kinase and orphan response regulator, function together as a cognate two-component regulatory system to directly activate transcription of several genes. One of these targets, agrB1D1, encodes gene products that synthesize and export a small quorum-sensing peptide, AgrD1, which positively influences expression of early sporulation genes. Another target, a small regulatory RNA now known as SrsR, impacts later stages of sporulation through an unknown regulatory mechanism(s). Unlike Agr systems in many organisms, AgrD1 does not activate the RgaS-RgaR two-component system, and thus, is not responsible for autoregulating its own production. Altogether, we demonstrate that C. difficile utilizes a conserved two-component system that is uncoupled from quorum-sensing to promote sporulation through two distinct regulatory pathways.
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Affiliation(s)
- Adrianne N. Edwards
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, GA, USA
| | - Shonna M. McBride
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, GA, USA
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